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Thomas Ioerger - Publications

Affiliations: 
Texas A & M University, College Station, TX, United States 
Area:
Computer Science
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. Plos Computational Biology. 20: e1011408. PMID 38768228 DOI: 10.1371/journal.pcbi.1011408  0.724
2023 Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response based model for statistical analysis of chemical genetic interactions in CRISPRi libraries. Biorxiv : the Preprint Server For Biology. PMID 37577548 DOI: 10.1101/2023.08.03.551759  0.716
2022 Ioerger TR. Analysis of Gene Essentiality from TnSeq Data Using Transit. Methods in Molecular Biology (Clifton, N.J.). 2377: 391-421. PMID 34709629 DOI: 10.1007/978-1-0716-1720-5_22  0.372
2021 Choudhery S, Brown AJ, Akusobi C, Rubin EJ, Sassetti CM, Ioerger TR. Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets. Msystems. e0087621. PMID 34665010 DOI: 10.1128/mSystems.00876-21  0.316
2021 Dutta E, DeJesus MA, Ruecker N, Zaveri A, Koh EI, Sassetti CM, Schnappinger D, Ioerger TR. An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence. Plos One. 16: e0257911. PMID 34597304 DOI: 10.1371/journal.pone.0257911  0.728
2019 Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR. Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. Bmc Bioinformatics. 20: 603. PMID 31752678 DOI: 10.1186/S12859-019-3156-Z  0.708
2019 Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, de Jong B, Rigouts L, Sloutsky A, Kaur D, Sunyaev S, van Soolingen D, Shendure J, Sacchettini J, Murray M. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nature Communications. 10: 2128. PMID 31086182 DOI: 10.1038/S41467-019-10110-6  0.383
2018 Tiwari D, Park SW, Essawy MM, Dawadi S, Mason A, Nandakumar M, Zimmerman M, Mina M, Ho HP, Engelhart CA, Ioerger T, Sacchettini JC, Rhee K, Ehrt S, Aldrich CC, et al. Targeting protein biotinylation enhances tuberculosis chemotherapy. Science Translational Medicine. 10. PMID 29695454 DOI: 10.1126/Scitranslmed.Aal1803  0.331
2018 Negri A, Javidnia P, Mu R, Zhang X, Vendome J, Gold B, Roberts J, Barman D, Ioerger T, Sacchettini JC, Jiang X, Burns-Huang K, Warrier T, Ling Y, Warren JD, et al. Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis. Acs Infectious Diseases. PMID 29465985 DOI: 10.1021/Acsinfecdis.7B00111  0.317
2017 Xu W, DeJesus MA, Rücker N, Engelhart CA, Wright MG, Healy C, Lin K, Wang R, Park SW, Ioerger TR, Schnappinger D, Ehrt S. Chemical genomic interaction profiling reveals determinants of intrinsic antibiotic resistance in Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy. PMID 28893793 DOI: 10.1128/Aac.01334-17  0.709
2017 DeJesus MA, Nambi S, Smith CM, Baker RE, Sassetti CM, Ioerger TR. Statistical analysis of genetic interactions in Tn-Seq data. Nucleic Acids Research. PMID 28334803 DOI: 10.1093/Nar/Gkx128  0.72
2017 DeJesus MA, Gerrick ER, Xu W, Park SW, Long JE, Boutte CC, Rubin EJ, Schnappinger D, Ehrt S, Fortune SM, Sassetti CM, Ioerger TR. Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis. Mbio. 8. PMID 28096490 DOI: 10.1128/Mbio.02133-16  0.716
2017 Maxwell S, Wallis D, Zhou N, Baker D, Mousavi-Fard S, Loesch K, Galaviz S, Sun Q, Threadgill D, Rojas C, O'Brien M, Clubb F, Ioerger T, DeJesus M, Dong W, et al. DEVELOPMENT OF NOVEL, NON-TOXIC RIFAMYCINS THAT REVERSE DRUG RESISTANCE IN DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) Hematological Oncology. 35: 253-254. DOI: 10.1002/hon.2438_118  0.649
2016 Korte J, Alber M, Trujillo CM, Syson K, Koliwer-Brandl H, Deenen R, Köhrer K, DeJesus MA, Hartman T, Jacobs WR, Bornemann S, Ioerger TR, Ehrt S, Kalscheuer R. Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice. Plos Pathogens. 12: e1006043. PMID 27936238 DOI: 10.1371/Journal.Ppat.1006043  0.707
2016 Orsini CA, Setlow B, DeJesus M, Galaviz S, Loesch K, Ioerger T, Wallis D. Behavioral and transcriptomic profiling of mice null for Lphn3, a gene implicated in ADHD and addiction. Molecular Genetics & Genomic Medicine. 4: 322-43. PMID 27247960 DOI: 10.1002/Mgg3.207  0.675
2016 Almeida D, Ioerger T, Tyagi S, Li SY, Mdluli K, Andries K, Grosset J, Sacchettini J, Nuermberger E. Mutations in pepQ Confer Low-level Resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy. PMID 27185800 DOI: 10.1128/Aac.00753-16  0.336
2016 DeJesus MA, Ioerger TR. Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. Journal of Bioinformatics and Computational Biology. 1642004. PMID 26932272 DOI: 10.1142/S021972001642004X  0.722
2015 Maksymiuk C, Ioerger T, Balakrishnan A, Bryk R, Rhee K, Sacchettini J, Nathan C. Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of rv1248c, encoding 2-hydroxy-3-oxoadipate synthase. Tuberculosis (Edinburgh, Scotland). 95: 689-94. PMID 26547230 DOI: 10.1016/J.Tube.2015.08.009  0.365
2015 DeJesus MA, Ambadipudi C, Baker R, Sassetti C, Ioerger TR. TRANSIT - A Software Tool for Himar1 TnSeq Analysis. Plos Computational Biology. 11: e1004401. PMID 26447887 DOI: 10.1371/Journal.Pcbi.1004401  0.701
2015 DeJesus MA, Ioerger TR. Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 92-102. PMID 26357081 DOI: 10.1109/Tcbb.2014.2326857  0.736
2015 Loesch K, Galaviz S, Hamoui Z, Clanton R, Akabani G, Deveau M, DeJesus M, Ioerger T, Sacchettini JC, Wallis D. Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation-response genes. Plos One. 10: e0120534. PMID 25853515 DOI: 10.1371/Journal.Pone.0120534  0.71
2015 Wallis D, Loesch K, Galaviz S, Sun Q, DeJesus M, Ioerger T, Sacchettini JC. High-Throughput Differentiation and Screening of a Library of Mutant Stem Cell Clones Defines New Host-Based Genes Involved in Rabies Virus Infection. Stem Cells (Dayton, Ohio). 33: 2509-22. PMID 25752821 DOI: 10.1002/Stem.1983  0.707
2015 Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM. Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods in Molecular Biology (Clifton, N.J.). 1279: 79-95. PMID 25636614 DOI: 10.1007/978-1-4939-2398-4_6  0.733
2014 Odingo J, O'Malley T, Kesicki EA, Alling T, Bailey MA, Early J, Ollinger J, Dalai S, Kumar N, Singh RV, Hipskind PA, Cramer JW, Ioerger T, Sacchettini J, Vickers R, et al. Synthesis and evaluation of the 2,4-diaminoquinazoline series as anti-tubercular agents. Bioorganic & Medicinal Chemistry. 22: 6965-79. PMID 25456390 DOI: 10.1016/J.Bmc.2014.10.007  0.327
2013 DeJesus MA, Ioerger TR. A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. Bmc Bioinformatics. 14: 303. PMID 24103077 DOI: 10.1186/1471-2105-14-303  0.735
2013 DeJesus MA, Zhang YJ, Sassetti CM, Rubin EJ, Sacchettini JC, Ioerger TR. Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. Bioinformatics (Oxford, England). 29: 695-703. PMID 23361328 DOI: 10.1093/Bioinformatics/Btt043  0.723
2013 DeJesus MA, Sacchettini JC, Ioerger TR. Reannotation of translational start sites in the genome of Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland). 93: 18-25. PMID 23273318 DOI: 10.1016/J.Tube.2012.11.012  0.702
2013 Dejesus MA, Ioerger TR. Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 144-151. DOI: 10.1145/2506583.2506610  0.731
2012 Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, Korber B, Fortune S. Mycobacterium tuberculosis - Heterogeneity revealed through whole genome sequencing Tuberculosis. 92: 194-201. PMID 22218163 DOI: 10.1016/J.Tube.2011.11.003  0.35
2011 Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. Plos Pathogens. 7: e1002251. PMID 21980284 DOI: 10.1371/Journal.Ppat.1002251  0.733
2007 Gopal K, McKee E, Romo T, Pai R, Smith J, Sacchettini J, Ioerger T. Crystallographic protein model-building on the web. Bioinformatics (Oxford, England). 23: 375-7. PMID 17138588 DOI: 10.1093/Bioinformatics/Btl584  0.514
2007 Gopal K, Ioerger TR. Distance metric learning through optimization of ranking Proceedings - Ieee International Conference On Data Mining, Icdm. 201-206. DOI: 10.1109/ICDMW.2007.113  0.478
2006 Pai R, Sacchettini J, Ioerger T. Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach. Acta Crystallographica. Section D, Biological Crystallography. 62: 1012-21. PMID 16929102 DOI: 10.1107/S0907444906023158  0.321
2006 Gopal K, Romo TD, McKee EW, Pai R, Smith JN, Sacchettini JC, Ioerger TR. TEXTAL: Crystallographic protein model building using AI and pattern recognition Ai Magazine. 27: 15-24.  0.465
2006 Palmer V, Ioerger T. Coalition formation meets information theory Flairs 2006 - Proceedings of the Nineteenth International Florida Artificial Intelligence Research Society Conference. 2006: 98-103.  0.555
2005 Gopal K, Romo TD, Sacchettini JC, Ioerger TR. Determining relevant features to recognize electron density patterns in x-ray protein crystallography. Journal of Bioinformatics and Computational Biology. 3: 645-76. PMID 16108088 DOI: 10.1142/S0219720005001272  0.493
2005 Romo T, Gopal K, McKee E, Kanbi L, Pai R, Smith J, Sacchettini J, Ioerger T. TEXTAL: Al-based structural determination for X-ray protein crystallography Ieee Intelligent Systems. 20: 59-63. DOI: 10.1109/Mis.2005.114  0.47
2004 Gopal K, Romo TD, Sacchettini JC, Ioerger TR. Weighting features to recognize 3D patterns of electron density in X-ray protein crystallography. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 255-65. PMID 16448019  0.443
2004 Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC. Recent developments in the PHENIX software for automated crystallographic structure determination. Journal of Synchrotron Radiation. 11: 53-5. PMID 14646133 DOI: 10.1107/S0909049503024130  0.457
2004 Gopal K, Romo TD, Sacchettini JC, Ioerger TR. Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography Proceedings of the 2004 International Conference On Machine Learning and Applications, Icmla '04. 380-387.  0.48
2003 Widyantoro DH, Ioerger TR, Yen J. Tracking changes in user interests with a few relevance judgments International Conference On Information and Knowledge Management, Proceedings. 548-551.  0.608
2002 Widyantoro DH, Ioerger TR, Yen J. An incremental approach to building a cluster hierarchy Proceedings - Ieee International Conference On Data Mining, Icdm. 705-708.  0.605
2001 Hofle M, Linthicum DS, Ioerger T. Analysis of diversity of nucleotide and amino acid distributions in the VD and DJ joining regions in Ig heavy chains Molecular Immunology. 37: 827-835. PMID 11257304 DOI: 10.1016/S0161-5890(00)00110-3  0.323
2001 Widyantoro DH, Ioerger TR, Yen J. Learning user interest dynamics with a three-descriptor representation Journal of the American Society For Information Science and Technology. 52: 212-225. DOI: 10.1002/1532-2890(2000)9999:9999<::Aid-Asi1615>3.0.Co;2-O  0.603
2001 Widyantoro DH, Ioerger TR, Yen J. Learning User Interest Dynamics with a Three-Descriptor Representation Journal of the American Society For Information Science and Technology. 52: 212-225. DOI: 10.1002/1532-2890(2000)9999:9999<::AID-ASI1615>3.0.CO;2-O  0.603
2001 Yang L, Widyantoro DH, Ioerger T, Yen J. An entropy-based adaptive genetic algorithm for learning classification rules Proceedings of the Ieee Conference On Evolutionary Computation, Icec. 2: 790-796.  0.623
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